Hello
I'm in the process of setting up a docking run using chemical shifts, and are
running into problems with the generation of a input structure for one of the
proteins in the docking.
I'm docking 2 proteins, where one of the proteins is a Zinc-finger with 2 Zn2+
atoms, one coordinated by 4 Cys and the other one coordinated by 2 Cys & 2 His.
One histidine is coordinated by NE2 and the other by ND1.
Based on answers from the mailing list and examples, I modified a topology file
and parameter file for incorporating the two Zn.
Upon running the file (see below) I can successfully generate the psf-file and
a pdb-file. However, in the pdb-file, the Zn2+ and some N and C-terminal
residues gets coordinates -9999.9. I have tried fixing that by running
fixupCovalentGeom in the script, which causes the script to fail, saying
missing atoms.
What have I missed when setting up the protein and how can I fix this?
I also want to mutate one residue to another in order to generate my version of
the protein.
The topology file is based on toph19.ion, where I generated bonds and angles,
based upon how Zn2+ are handled in Aria/CNS. The file is as follows:
PRESidue ZNK
GROUP
delete atom 1HG end
MODIfy ATOM 1CB CHARge= 0.19 END
MODIfy ATOM 1SG TYPE=S CHARge=-0.19 END
ATOM 1ZN TYPE=ZN CHARGE=+2.0 END
GROUP
delete atom 2HG end
MODIfy ATOM 2CB CHARge= 0.19 END
MODIfy ATOM 2SG TYPE=S CHARge=-0.19 END
GROUP
delete atom 3HG end
MODIfy ATOM 3CB CHARge= 0.19 END
MODIfy ATOM 3SG TYPE=S CHARge=-0.19 END
GROUP
delete atom 4HG end
MODIfy ATOM 4CB CHARge= 0.19 END
MODIfy ATOM 4SG TYPE=S CHARge=-0.19 END
ADD BOND 1ZN 1SG
ADD BOND 1ZN 2SG
ADD BOND 1ZN 3SG
ADD BOND 1ZN 4SG
ADD ANGLe 1CB 1SG 1ZN
ADD ANGLe 2CB 2SG 1ZN
ADD ANGLe 3CB 3SG 1ZN
ADD ANGLe 4CB 4SG 1ZN
ADD ANGLe 1SG 2SG 1ZN
ADD ANGLe 1SG 3SG 1ZN
ADD ANGLe 1SG 4SG 1ZN
ADD ANGLe 2SG 3SG 1ZN
ADD ANGLe 2SG 4SG 1ZN
ADD ANGLe 3SG 4SG 1ZN
END
PRESidue C2HED
GROUP
delete atom 1HG end
MODIfy ATOM 1CB CHARge= 0.19 END
MODIfy ATOM 1SG TYPE=S CHARge=-0.19 END
ATOM 1ZN TYPE=ZN CHARGE=+2.0 END
GROUP
delete atom 2HG end
MODIfy ATOM 2CB CHARge= 0.19 END
MODIfy ATOM 2SG TYPE=S CHARge=-0.19 END
GROUP
MODIFY ATOM 3ND1 TYPE=NR CHARge=-0.40 END
GROUP
MODIFY ATOM 4NE2 TYPE=NR CHARge=-0.40 END
add bond 1ZN 1SG
add bond 1ZN 2SG
add bond 1ZN 3ND1
add bond 1ZN 4NE2
add angle 1SG 1ZN 2SG
add angle 1SG 1ZN 3ND1
add angle 1SG 1ZN 4NE2
add angle 2SG 1ZN 3ND1
add angle 2SG 1ZN 4NE2
add angle 3ND1 1ZN 4NE2
add angle 1ZN 1SG 1CB
add angle 1ZN 2SG 2CB
add angle 1ZN 3ND1 3CG
add angle 1ZN 3ND1 3CE1
add angle 1ZN 4NE2 4CG
add angle 1ZN 4NE2 4CD2
END
RESIdue ZN {* zinc *}
GROUP
ATOM ZN TYPE=ZN CHARGE=+2.0 END
END
and the parameter file is:
bonds S ZN 500.0 2.30
BOND NR ZN 500.000 2.00
angles S ZN S 500.0 109.5
angles ZN S CH2E 70.0 120.0
angles ZN S CT 70.0 120.0
angles S ZN NR 500.0 109.5
angles NR ZN NR 500 109.5
ANGLes ZN NR CR1E 500.00 120.0000
ANGLes ZN NR CRH 500.00 120.0000
ANGLes ZN NR C5 500.00 120.0000
! eps sigma eps(1:4) sigma(1:4)
! (kcal/mol) (A)
! ---------------------------------------
NONBonded ZN 0.0430 3.3676 0.0430 3.3676 ! garbage
I generate the psf-file using the following python-script, where I first patch
histidine residues to the correct protonation and then I add the Zn-patches:
xplor.parseArguments()
import protocol
protocol.loadPDB("1tota_cns.pdb")
import psfGen
protocol.initTopology("toph19.ion")
protocol.initTopology("toph19.his")
protocol.initParams("param19.ion")
protocol.initParams("parhcsdx.pro")
xplor.command("""
topology
AUTO ANGLe=False DIHEdral=False END
end
patch HISE
reference=nil=( resid 242 )
end
patch HISD
reference=nil=( resid 240 )
end
patch ZNK
reference=1=( resid 209 )
reference=2=( resid 212 )
reference=3=( resid 231 )
reference=4=( resid 234 )
end
patch C2HED
reference=1=( resid 222 )
reference=2=( resid 225 )
reference=3=( resid 242 )
reference=4=( resid 240 )
end
""")
xplor.command("write psf output=1tota_cns_zn.psf end")
from pdbTool import PDBTool
PDBTool("test.pdb").write()
Best Regards
Carl Diehl
Post-Doc
NNF CPR
Copenhagen university, Denmark
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